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Erdoğan ÖŞ, Ödemiş DA, Kayım ZY, Gürbüz O, Tunçer ŞB, Kılıç S, Çelik B, Tuncer S, Bay SB, Kebudi R, Yazıcı H. Investigation of the methylation changes in the promoter region of RB1 gene in retinoblastoma: Unraveling the epigenetic puzzle in retinoblastoma. Pathol Res Pract 2024; 253:154939. [PMID: 38006838 DOI: 10.1016/j.prp.2023.154939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/27/2023]
Abstract
Retinoblastoma is an infrequent neoplasm that arises during childhood from retinal nerve cells and is attributed to the biallelic inactivation of the RB1 gene. In conjunction with anatomical anomalies, it is widely acknowledged that epigenetic modifications play a significant role in the pathogenesis of cancer. The association between methylation of the RB1 gene promoter and tumor formation has been established; however, there is currently no scholarly evidence to substantiate the claim that it is responsible for the inheritance of retinoblastoma. The initial hypothesis posited for this work was that familial retinoblastoma disease would be similarly observed in cases with RB1 promotor gene methylation, akin to RB1 mutations. The RB1 gene promoter region was subjected to methylation screening using real-time PCR in individuals diagnosed with familial retinoblastoma but lacking RB1 mutations. The study involved a comparison of the germline methylation status of the RB1 gene in the peripheral blood samples of 50 retinoblastoma patients and 52 healthy individuals. The healthy individuals were carefully selected to match the retinoblastoma patients in terms of age, sex, and ethnicity. The data obtained from both groups were subjected to statistical analysis. The study revealed that the methylation level in a cohort of 50 individuals diagnosed with retinoblastoma and 52 healthy control participants was determined to be 36.1% and 33.9%, respectively. As a result, there was no statistically significant disparity observed in RB1 promoter methylation between the patient and control groups (p = 0.126). The methylation of the promoter region of the RB1 gene in familial retinoblastoma does not exert any influence on the hereditary transmission of the disease.
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Affiliation(s)
- Özge Şükrüoğlu Erdoğan
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey.
| | - Demet Akdeniz Ödemiş
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey
| | - Zübeyde Yalnız Kayım
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey
| | - Orkun Gürbüz
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey; İstinye University, Vocational School of Health Care Services
| | - Şeref Buğra Tunçer
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey
| | - Seda Kılıç
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey
| | - Betül Çelik
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey
| | - Samuray Tuncer
- Department of Ophthalmology, Istanbul Medical Faculty, Istanbul University, Fatih, 34093 Istanbul, Turkey
| | - Sema Büyükkapu Bay
- Department of Pediatric and Hematologic Oncology, Oncology Institute, Istanbul University, Fatih, 34093 Istanbul, Turkey
| | - Rejin Kebudi
- Department of Pediatric and Hematologic Oncology, Oncology Institute, Istanbul University, Fatih, 34093 Istanbul, Turkey
| | - Hülya Yazıcı
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey; Arel University Faculty of Medicine, Department of Basic Medical Sciences / Medical Biology
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Qiu L, Sheng P, Wang X. Identification of Metabolic Syndrome-Related miRNA-mRNA Regulatory Networks and Key Genes Based on Bioinformatics Analysis. Biochem Genet 2023; 61:428-447. [PMID: 35877019 DOI: 10.1007/s10528-022-10257-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/18/2022] [Indexed: 01/24/2023]
Abstract
Metabolic syndrome, which affects approximately one-quarter of the world's population, is a combination of multiple traits and is associated with high all-cause mortality, increased cancer risk, and other hazards. It has been shown that the epigenetic functions of miRNAs are closely related to metabolic syndrome, but epigenetic studies have not yet fully elucidated the regulatory network and key genes associated with metabolic syndrome. To perform data analysis and screening of potential differentially expressed target miRNAs, mRNAs and genes based on a bioinformatics approach using a metabolic syndrome mRNA and miRNA gene microarray, leading to further analysis and identification of metabolic syndrome-related miRNA-mRNA regulatory networks and key genes. The miRNA gene set (GSE98896) and mRNA gene set (GSE98895) of peripheral blood samples from patients with metabolic syndrome from the GEO database were screened, and set|logFC|> 1 and adjusted P < 0.05 were used to identify the differentially expressed miRNAs and mRNAs. Differentially expressed miRNA transcription factors were predicted using FunRich software and subjected to GO and KEGG enrichment analysis. Next, biological process enrichment analysis of differentially expressed mRNAs was performed with Metascape. Differentially expressed miRNAs and mRNAs were identified and visualized as miRNA-mRNA regulatory networks based on the complementary pairing principle. Data analysis of genome-wide metabolic syndrome-related mRNAs was performed using the gene set enrichment analysis (GSEA) database. Finally, further WGCNA of the set of genes most closely associated with metabolic syndrome was performed to validate the findings. A total of 217 differentially expressed mRNAs and 158 differentially expressed miRNAs were identified by screening the metabolic syndrome miRNA and mRNA gene sets, and these molecules mainly included transcription factors, such as SP1, SP4, and EGR1, that function in the IL-17 signalling pathway; cytokine-cytokine receptor interaction; proteoglycan syndecan-mediated signalling events; and the glypican pathway, which is involved in the inflammatory response and glucose and lipid metabolism. miR-34C-5P, which was identified by constructing a miRNA-mRNA regulatory network, could regulate DPYSL4 expression to influence insulin β-cells, the inflammatory response and glucose oxidative catabolism. Based on GSEA, metabolic syndrome is known to be closely related to oxidative phosphorylation, DNA repair, neuronal damage, and glycolysis. Finally, RStudio and DAVID were used to perform WGCNA of the gene sets most closely associated with metabolic syndrome, and the results further validated the conclusions. Metabolic syndrome is a common metabolic disease worldwide, and its mechanism of action is closely related to the inflammatory response, glycolipid metabolism, and impaired mitochondrial function. miR-34C-5P can regulate DPYSL4 expression and can be a potential research target. In addition, UQCRQ and NDUFA8 are core genes of oxidative phosphorylation and have also been identified as potential targets for the future treatment of metabolic syndrome.
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Affiliation(s)
- Lingyan Qiu
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210029, China.,The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Pei Sheng
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210029, China.,The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Xu Wang
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210029, China. .,The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China.
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Ormazabal V, Nair S, Carrión F, Mcintyre HD, Salomon C. The link between gestational diabetes and cardiovascular diseases: potential role of extracellular vesicles. Cardiovasc Diabetol 2022; 21:174. [PMID: 36057662 PMCID: PMC9441052 DOI: 10.1186/s12933-022-01597-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/05/2022] [Indexed: 11/25/2022] Open
Abstract
Extracellular vesicles are critical mediators of cell communication. They encapsulate a variety of molecular cargo such as proteins, lipids, and nucleic acids including miRNAs, lncRNAs, circular RNAs, and mRNAs, and through transfer of these molecular signals can alter the metabolic phenotype in recipient cells. Emerging studies show the important role of extracellular vesicle signaling in the development and progression of cardiovascular diseases and associated risk factors such as type 2 diabetes and obesity. Gestational diabetes mellitus (GDM) is hyperglycemia that develops during pregnancy and increases the future risk of developing obesity, impaired glucose metabolism, and cardiovascular disease in both the mother and infant. Available evidence shows that changes in maternal metabolism and exposure to the hyperglycemic intrauterine environment can reprogram the fetal genome, leaving metabolic imprints that define life-long health and disease susceptibility. Understanding the factors that contribute to the increased susceptibility to metabolic disorders of children born to GDM mothers is critical for implementation of preventive strategies in GDM. In this review, we discuss the current literature on the fetal programming of cardiovascular diseases in GDM and the impact of extracellular vesicle (EV) signaling in epigenetic programming in cardiovascular disease, to determine the potential link between EV signaling in GDM and the development of cardiovascular disease in infants.
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Affiliation(s)
- Valeska Ormazabal
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, UQ Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of Medicine + Biomedical Sciences, The University of Queensland, Building 71/918, Herston, QLD, 4029, Australia.,Faculty of Biological Sciences, Pharmacology Department, University of Concepcion, Concepción, Chile
| | - Soumyalekshmi Nair
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, UQ Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of Medicine + Biomedical Sciences, The University of Queensland, Building 71/918, Herston, QLD, 4029, Australia
| | - Flavio Carrión
- Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad del Alba, Santiago, Chile
| | - H David Mcintyre
- Mater Research, Faculty of Medicine, University of Queensland, Mater Health, South Brisbane, Australia
| | - Carlos Salomon
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, UQ Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of Medicine + Biomedical Sciences, The University of Queensland, Building 71/918, Herston, QLD, 4029, Australia. .,Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad del Alba, Santiago, Chile.
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Ghosh A, Ranjan N, Jiang L, Ansari AH, Degyatoreva N, Ahluwalia S, Arya DP, Maiti S. Fine-tuning miR-21 expression and inhibition of EMT in breast cancer cells using aromatic-neomycin derivatives. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:685-698. [PMID: 35070496 PMCID: PMC8763640 DOI: 10.1016/j.omtn.2021.12.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/17/2021] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRs) are a class of endogenously expressed non-coding RNAs that negatively regulate gene expression within cells and participate in maintaining cellular homeostasis. By targeting 3' UTRs of target genes, individual miRs can control a wide array of gene expressions. Previous research has shed light upon the fact that aberrantly expressed miRs within cells can pertain to diseased conditions, such as cancer. Malignancies caused due to miRs are because of the high expression of onco-miRs or feeble expression of tumor-suppressing miRs. Studies have also shown miRs to engage in epithelial to mesenchymal transition (EMT), which allows cancer cells to become more invasive and metastasize. miR-21 is an onco-miR highly expressed in breast cancer cells and targets protein PTEN, which abrogates EMT. Therefore, we discuss an approach where in-house-developed peptidic amino sugar molecules have been used to target pre-miR-21 to inhibit miR-21 biogenesis, and hence antagonize its tumor-causing effect and inhibit EMT. Our study shows that small-molecule-based fine-tuning of miR expression can cause genotypic as well as phenotypic changes and also reinstates the potential and importance of nucleic acid therapeutics.
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Affiliation(s)
- Arpita Ghosh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India.,Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Nihar Ranjan
- Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Liuwei Jiang
- Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Asgar Hussain Ansari
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India.,Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | | | - Shivaksh Ahluwalia
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India.,Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, Delhi 110016, India
| | - Dev P Arya
- Department of Chemistry, Clemson University, Clemson, SC 29634, USA.,NUBAD LLC, Greenville, SC 29605, USA
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India.,Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
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Ramzan F, Vickers MH, Mithen RF. Epigenetics, microRNA and Metabolic Syndrome: A Comprehensive Review. Int J Mol Sci 2021; 22:ijms22095047. [PMID: 34068765 PMCID: PMC8126218 DOI: 10.3390/ijms22095047] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Epigenetics refers to the DNA chemistry changes that result in the modification of gene transcription and translation independently of the underlying DNA coding sequence. Epigenetic modifications are reported to involve various molecular mechanisms, including classical epigenetic changes affecting DNA methylation and histone modifications and small RNA-mediated processes, particularly that of microRNAs. Epigenetic changes are reversible and are closely interconnected. They are recognised to play a critical role as mediators of gene regulation, and any alteration in these mechanisms has been identified to mediate various pathophysiological conditions. Moreover, genetic predisposition and environmental factors, including dietary alterations, lifestyle or metabolic status, are identified to interact with the human epigenome, highlighting the importance of epigenetic factors as underlying processes in the aetiology of various diseases such as MetS. This review will reflect on how both the classical and microRNA-regulated epigenetic changes are associated with the pathophysiology of metabolic syndrome. We will then focus on the various aspects of epigenetic-based strategies used to modify MetS outcomes, including epigenetic diet, epigenetic drugs, epigenome editing tools and miRNA-based therapies.
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DENG Z, GAO W, LUO W, AI L, HU M. Significant Association between Microrna Gene Polymorphisms and Type 2 Diabetes Mellitus Susceptibility in Asian Population: A Meta-Analysis. IRANIAN JOURNAL OF PUBLIC HEALTH 2020; 49:830-836. [PMID: 32953671 PMCID: PMC7475618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
BACKGROUND The gene polymorphisms in microRNA might relate to susceptibility of type 2 diabetes mellitus (T2DM). However, the results of existing studies were inconsistent and obscure. To investigate the precise associations between microRNA gene polymorphisms and T2DM risk, the present meta-analysis was performed. METHODS The literatures were searched from four electronic databases, PubMed, Embase, CNKI and Wan-fang. Subsequently, odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) were both used to evaluate the associations between two single nucleotide polymorphisms (SNPs) (microRNA146a rs2910164 (G>C), microRNA124a rs531564 (C>G)) and risk of T2DM in Asian population. RESULTS Totally, there were 4 studies included in our present analysis in the language of English and Chinese. There were partly significant associations between susceptibility of T2DM and SNPs (microRNA146a rs2910164 (G>C), microRNA124a rs531564 (C>G)). The G allele in microRNA146a rs2910164 (G>C) and C allele in microRNA124a rs531564 (C>G) both presented remarkably reduced risk of T2DM when compared with the healthy population. CONCLUSION The microRNA146a rs2910164 (G allele) and microRNA124a rs531564 (C allele) might function as protective factors in the pathogenetic process of T2DM in Asian population.
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Affiliation(s)
- Zhifang DENG
- Department of Pharmacy, The First College of Clinical Medical Science, China Three Gorges University & Yichang Central People’s Hospital, Yichang, 443000, China,Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei, China,Corresponding Author:
| | - Wenqi GAO
- Institute of Maternal and Child Health, Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430000, China,Department of Central Experimental Laboratory & Yichang Key Laboratory of Ischemic Cardiovascular and Cerebrovascular Disease Translational Medicine, The First College of Clinical Medical Science, China Three Gorges University & Yichang Central People’s Hospital, Yichang, 443003, China
| | - Wei LUO
- Department of Pharmacy, The First College of Clinical Medical Science, China Three Gorges University & Yichang Central People’s Hospital, Yichang, 443000, China
| | - Li AI
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Min HU
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei, China
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Tang Y, He X, Yuan R, Liu X, Zhao Y, Wang T, Chen H, Feng X. Logic-signal-based multiplex detection of MiRNAs with high tension hybridization and multiple signal amplification. Analyst 2020; 145:4314-4320. [PMID: 32400825 DOI: 10.1039/d0an00550a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multiplex miRNA detection scheme with simultaneous multiple signal output by single excitation has been reported.
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Affiliation(s)
- Yaqin Tang
- Department of Pharmaceutical Sciences
- Chongqing University
- Chongqing
- China
| | - Xiao He
- Department of Pharmaceutical Sciences
- Chongqing University
- Chongqing
- China
| | - Rui Yuan
- Chongqing University Cancer Hospital
- Chongqing Cancer Hospital
- Chongqing
- China
| | - Xingming Liu
- Chongqing University Cancer Hospital
- Chongqing Cancer Hospital
- Chongqing
- China
| | - Yi Zhao
- Chongqing University Cancer Hospital
- Chongqing Cancer Hospital
- Chongqing
- China
| | - Tingting Wang
- Biochemistry and Molecular Biology Laboratory
- Experimental Teaching and Management Center
- Chongqing Medical University
- Chongqing
- China
| | - Hui Chen
- Department of Pharmaceutical Sciences
- Chongqing University
- Chongqing
- China
| | - Xuli Feng
- Department of Pharmaceutical Sciences
- Chongqing University
- Chongqing
- China
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Smail HO. The epigenetics of diabetes, obesity, overweight and cardiovascular disease. AIMS GENETICS 2019; 6:36-45. [PMID: 31663031 PMCID: PMC6803788 DOI: 10.3934/genet.2019.3.36] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023]
Abstract
The objectives of this review were once to understand the roles of the epigenetics mechanism in different types of diabetes, obesity, overweight, and cardiovascular disease. Epigenetics represents a phenomenon of change heritable phenotypic expression of genetic records taking place except changes in DNA sequence. Epigenetic modifications can have an impact on a whole of metabolic disease with the aid of specific alteration of candidate genes based totally on the change of the target genes. In this review, I summarized the new findings in DNA methylation, histone modifications in each type of diabetes (type 1 and type 2), obesity, overweight, and cardiovascular disease. The involvement of histone alterations and DNA methylation in the development of metabolic diseases is now widely accepted recently many novel genes have been demonstrated that has roles in diabetes pathway and it can be used for detection prediabetic; however Over the modern-day years, mass spectrometry-based proteomics techniques positioned and mapped one-of a kind range of histone modifications linking obesity and metabolic diseases. The main point of these changes is rapidly growing; however, their points and roles in obesity are no longer properly understood in obesity. Furthermore, epigenetic seen in cardiovascular treatment revealed a massive quantity of modifications affecting the improvement and development of cardiovascular disease. In addition, epigenetics are moreover involved in cardiovascular risk factors such as smoking. The aberrant epigenetic mechanisms that make a contribution to cardiovascular disease.
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Affiliation(s)
- Harem Othman Smail
- Department of Biology, Faculty of science and health, Koya University Koya KOY45, Kurdistan Region-F.R. Iraq
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Herrera-Moreno JF, Medina-Díaz IM, Bernal-Hernández YY, Ramos KS, Alvarado-Cruz I, Quintanilla-Vega B, González-Arias CA, Barrón-Vivanco BS, Rojas-García AE. Modified CDKN2B (p15) and CDKN2A (p16) DNA methylation profiles in urban pesticide applicators. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:15124-15135. [PMID: 30924039 DOI: 10.1007/s11356-019-04658-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Gene-specific changes in DNA methylation by pesticides in occupationally exposed populations have not been studied extensively. Of particular concern are changes in the methylation profile of tumor-suppressor, such as CDKN2B and CDKN2A, genes involved in oncogenesis. The aim of this study was to evaluate the methylation profiles of CDKN2B and CDKN2A genes in urban pesticide applicators and their relationship with occupational exposure to pesticides. A cross-sectional study was conducted in 186 urban pesticide applicators (categorized as high or moderate exposures) and 102 participants without documented occupational exposures to pesticides. Acute and chronic pesticide exposures were evaluated by direct measurement of urinary dialkylphosphates, organophosphate metabolites, and a structured questionnaire, respectively. Anthropometric characteristics, diet, clinical histories, and other variables were estimated through a validated self-reported survey. DNA methylation was determined by pyrosequencing of bisulfite-treated DNA. Decreased DNA methylation of the CDKN2B gene was observed in pesticide-exposed groups compared to the non-exposed group. In addition, increased methylation of the CDKN2A promoter was observed in the moderate-exposure group compared to the non-exposed group. Bivariate analysis showed an association between CDKN2B methylation and pesticide exposure, general characteristics, smoking status, and micronutrients, while changes in CDKN2A methylation were associated with pesticide exposure, sex, educational level, body mass index, smoking status, supplement intake, clinical parameters, and caffeine consumption. These data suggest that pesticide exposure modifies the methylation pattern of CDKN2B and CDKN2A genes and raise important questions about the role that these changes may play in the regulation of cell cycle activities, senescence, and aging.
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Affiliation(s)
- José Francisco Herrera-Moreno
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000, Tepic, Nayarit, Mexico
- Posgrado en Ciencias Biológico Agropecuarias, Unidad Académica de Agricultura, Km. 9 Carretera Tepic-Compostela, Xalisco, Nayarit, Mexico
| | - Irma Martha Medina-Díaz
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000, Tepic, Nayarit, Mexico
| | - Yael Yvette Bernal-Hernández
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000, Tepic, Nayarit, Mexico
| | - Kenneth S Ramos
- Department of Medicine, Division of Clinical Support and Data Analytics, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Isabel Alvarado-Cruz
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Betzabet Quintanilla-Vega
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Cyndia Azucena González-Arias
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000, Tepic, Nayarit, Mexico
| | - Briscia Socorro Barrón-Vivanco
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000, Tepic, Nayarit, Mexico
| | - Aurora Elizabeth Rojas-García
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000, Tepic, Nayarit, Mexico.
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Hebbar P, Abubaker JA, Abu-Farha M, Tuomilehto J, Al-Mulla F, Thanaraj TA. A Perception on Genome-Wide Genetic Analysis of Metabolic Traits in Arab Populations. Front Endocrinol (Lausanne) 2019; 10:8. [PMID: 30761081 PMCID: PMC6362414 DOI: 10.3389/fendo.2019.00008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/09/2019] [Indexed: 12/16/2022] Open
Abstract
Despite dedicated nation-wide efforts to raise awareness against the harmful effects of fast-food consumption and sedentary lifestyle, the Arab population continues to struggle with an increased risk for metabolic disorders. Unlike the European population, the Arab population lacks well-established genetic risk determinants for metabolic disorders, and the transferability of established risk loci to this population has not been satisfactorily demonstrated. The most recent findings have identified over 240 genetic risk loci (with ~400 independent association signals) for type 2 diabetes, but thus far only 25 risk loci (ADAMTS9, ALX4, BCL11A, CDKAL1, CDKN2A/B, COL8A1, DUSP9, FTO, GCK, GNPDA2, HMG20A, HNF1A, HNF1B, HNF4A, IGF2BP2, JAZF1, KCNJ11, KCNQ1, MC4R, PPARγ, SLC30A8, TCF7L2, TFAP2B, TP53INP1, and WFS1) have been replicated in Arab populations. To our knowledge, large-scale population- or family-based association studies are non-existent in this region. Recently, we conducted genome-wide association studies on Arab individuals from Kuwait to delineate the genetic determinants for quantitative traits associated with anthropometry, lipid profile, insulin resistance, and blood pressure levels. Although these studies led to the identification of novel recessive variants, they failed to reproduce the established loci. However, they provided insights into the genetic architecture of the population, the applicability of genetic models based on recessive mode of inheritance, the presence of genetic signatures of inbreeding due to the practice of consanguinity, and the pleiotropic effects of rare disorders on complex metabolic disorders. This perspective presents analysis strategies and study designs for identifying genetic risk variants associated with diabetes and related traits in Arab populations.
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Affiliation(s)
- Prashantha Hebbar
- Genetics and Bioinformatics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
- Doctoral Program in Population Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jehad Ahmed Abubaker
- Genetics and Bioinformatics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Mohamed Abu-Farha
- Genetics and Bioinformatics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Jaakko Tuomilehto
- Genetics and Bioinformatics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Genetics and Bioinformatics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
- *Correspondence: Fahd Al-Mulla
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11
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Ruiz-Tórtola Á, Prats-Quílez F, González-Lucas D, Bañuls MJ, Maquieira Á, Wheeler G, Dalmay T, Griol A, Hurtado J, Bohlmann H, Götzen R, García-Rupérez J. Experimental study of the evanescent-wave photonic sensors response in presence of molecular beacon conformational changes. JOURNAL OF BIOPHOTONICS 2018; 11:e201800030. [PMID: 29664230 DOI: 10.1002/jbio.201800030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/12/2018] [Indexed: 05/20/2023]
Abstract
An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes-upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors-is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5' termination. Those MBs incorporate a biotin moiety close to their 3' termination in order to selectively bind a streptavidin molecule to them. The different photonic sensing responses obtained toward the target oligonucleotide detection, when the streptavidin molecule was bound to the MB probes or not, demonstrate the conformational change suffered by the MB upon hybridization, which promotes the displacement of the streptavidin molecule away from the surface of the photonic sensing structure.
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Affiliation(s)
- Ángela Ruiz-Tórtola
- Nanophotonics Technology Center, Universitat Politècnica de València, Valencia, Spain
| | | | - Daniel González-Lucas
- Departamento de Química, IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Valencia, Spain
| | - María-José Bañuls
- Departamento de Química, IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Valencia, Spain
| | - Ángel Maquieira
- Departamento de Química, IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Valencia, Spain
| | - Guy Wheeler
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Amadeu Griol
- Nanophotonics Technology Center, Universitat Politècnica de València, Valencia, Spain
| | - Juan Hurtado
- Nanophotonics Technology Center, Universitat Politècnica de València, Valencia, Spain
| | - Helge Bohlmann
- microTEC Gesellschaft für Mikrotechnologie mbH, Duisburg, Germany
| | - Reiner Götzen
- microTEC Gesellschaft für Mikrotechnologie mbH, Duisburg, Germany
| | - Jaime García-Rupérez
- Nanophotonics Technology Center, Universitat Politècnica de València, Valencia, Spain
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12
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Role of MIR-196a2 Gene Polymorphism in Some Hormonal and Physiological Parameters Levels in Type 2 Diabetic Patients. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.3.58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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13
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Hemerich D, van Setten J, Tragante V, Asselbergs FW. Integrative Bioinformatics Approaches for Identification of Drug Targets in Hypertension. Front Cardiovasc Med 2018; 5:25. [PMID: 29670885 PMCID: PMC5894467 DOI: 10.3389/fcvm.2018.00025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/12/2018] [Indexed: 01/11/2023] Open
Abstract
High blood pressure or hypertension is an established risk factor for a myriad of cardiovascular diseases. Genome-wide association studies have successfully found over nine hundred loci that contribute to blood pressure. However, the mechanisms through which these loci contribute to disease are still relatively undetermined as less than 10% of hypertension-associated variants are located in coding regions. Phenotypic cell-type specificity analyses and expression quantitative trait loci show predominant vascular and cardiac tissue involvement for blood pressure-associated variants. Maps of chromosomal conformation and expression quantitative trait loci (eQTL) in critical tissues identified 2,424 genes interacting with blood pressure-associated loci, of which 517 are druggable. Integrating genome, regulome and transcriptome information in relevant cell-types could help to functionally annotate blood pressure associated loci and identify drug targets.
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Affiliation(s)
- Daiane Hemerich
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Vinicius Tragante
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, Netherlands.,Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, United Kingdom.,Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, United Kingdom
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14
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Ruiz-Tórtola Á, Prats-Quílez F, González-Lucas D, Bañuls MJ, Maquieira Á, Wheeler G, Dalmay T, Griol A, Hurtado J, García-Rupérez J. High sensitivity and label-free oligonucleotides detection using photonic bandgap sensing structures biofunctionalized with molecular beacon probes. BIOMEDICAL OPTICS EXPRESS 2018; 9:1717-1727. [PMID: 29675313 PMCID: PMC5905917 DOI: 10.1364/boe.9.001717] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/13/2018] [Accepted: 01/24/2018] [Indexed: 05/20/2023]
Abstract
A label-free sensor, based on the combination of silicon photonic bandgap (PBG) structures with immobilized molecular beacon (MB) probes, is experimentally developed. Complementary target oligonucleotides are specifically recognized through hybridization with the MB probes on the surface of the sensing structure. This combination of PBG sensing structures and MB probes demonstrates an extremely high sensitivity without the need for complex PCR-based amplification or labelling methods.
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Affiliation(s)
- Ángela Ruiz-Tórtola
- Nanophotonics Technology Center, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Francisco Prats-Quílez
- Nanophotonics Technology Center, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Daniel González-Lucas
- IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento de Química, Universitat Politècnica de València, 46022 Valencia, Spain
| | - María-José Bañuls
- IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento de Química, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ángel Maquieira
- IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento de Química, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Guy Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Amadeu Griol
- Nanophotonics Technology Center, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Juan Hurtado
- Nanophotonics Technology Center, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Jaime García-Rupérez
- Nanophotonics Technology Center, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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15
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McCormick TM, Carvalho MDGDC. Using Methylation-Specific PCR to Study RB1 Promoter Hypermethylation. Methods Mol Biol 2018; 1726:29-34. [PMID: 29468541 DOI: 10.1007/978-1-4939-7565-5_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It has increasingly been considered crucial the understanding of DNA methylation of Tumor Suppressor Gene (TSG) promoters, such as that of retinoblastoma 1 gene (RB1), and its role during carcinogenesis. We present a detailed and optimized protocol of the methylation-specific PCR (MSP) technique to study RB1 gene promoter hypermethylation.
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Affiliation(s)
- Thaís M McCormick
- Laboratory of Molecular Pathology, Department of Pathology, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Maria Da Glória Da C Carvalho
- Laboratory of Molecular Pathology, Department of Pathology, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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16
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Zhang R, Li J, Huang T, Wang X. Danggui buxue tang suppresses high glucose-induced proliferation and extracellular matrix accumulation of mesangial cells via inhibiting lncRNA PVT1. Am J Transl Res 2017; 9:3732-3740. [PMID: 28861164 PMCID: PMC5575187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Danggui Buxue Tang (DBT), a traditional Chinese medicine decoction, has been proven to have satisfactory effects on treating diabetic nephropathy (DN). In this study, we explored the potential underlying mechanism of DBT in DN treatment. METHODS The DBT-containning serum was prepared by intragastric administration with DBT for rats. The levels of fibronectin (FN), laminin (LN) and collagen IV (COL IV) and TGF-β1 protein secreted in cell culture medium were determined by ELISA assay. The mRNA and protein expression of related molecule was measured using qRT-PCR and western blotting. MTT assay was applied to test MCs proliferation. RESULTS DBT has a negative effect on the high glucose (HG)-induced proliferation and extracellular matrix (ECM) accumulation of mesangial cells (MCs). Further research showed that DBT reduced the acetylation level of histone H3 at the site of PVT1 promoter to promote PVT1 downregulation, which was accompanied by a decrease in TGF-β and c-myc expression. Moreover, PVT1 overexpression significantly enhanced cell viability and promoted the expression levels of TGF-β1 and c-myc. Furthermore, PVT1 overexpression significantly reversed the inhibition of DBT on HG-induced cell viability and ECM accumulation and also lifted the effect of DBT on TGF-β1 and c-myc expression. CONCLUSION DBT inhibited TGF-β1 and c-myc expression through downregulating PVT1, and thus attenuated MCs excessive proliferation and ECM accumulation in DN.
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Affiliation(s)
- Rui Zhang
- Department of Endocrinology, The Affiliated Hospital of Changchun University of Chinese MedicineChangchun 130021, Jilin Province, People’s Republic of China
| | - Jinbo Li
- Department of Endocrinology, The Affiliated Hospital of Changchun University of Chinese MedicineChangchun 130021, Jilin Province, People’s Republic of China
| | - Tao Huang
- Department of Emergency Physicians, The Affiliated Hospital of Changchun University of Chinese MedicineChangchun 130021, Jilin Province, People’s Republic of China
| | - Xiuge Wang
- Department of Endocrinology, The Affiliated Hospital of Changchun University of Chinese MedicineChangchun 130021, Jilin Province, People’s Republic of China
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17
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Sharma D, Bhattacharya P, Kalia K, Tiwari V. Diabetic nephropathy: New insights into established therapeutic paradigms and novel molecular targets. Diabetes Res Clin Pract 2017; 128:91-108. [PMID: 28453961 DOI: 10.1016/j.diabres.2017.04.010] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 04/07/2017] [Indexed: 02/06/2023]
Abstract
Diabetic nephropathy is one of the most prevalent microvascular complication in patients suffering from diabetes and is reported to be the major cause of renal failure when compared to any other kidney disease. Currently, available therapies provide only symptomatic relief and unable to treat the underlying pathophysiology of diabetic nephropathy. This review will explore new insights into the established therapeutic paradigms targeting oxidative stress, inflammation and endoplasmic reticulum stress with the focus on recent clinical developments. Apart from this, the involvement of novel cellular and molecular mechanisms including the role of endothelin-receptor antagonists, Wnt signaling pathway, epigenetics and micro RNA is also discussed so that key molecular switches involved in the pathogenesis of diabetic nephropathy can be identified. Elucidating new molecular pathways will help in the development of novel therapeutics for the prevention and treatment of diabetic nephropathy.
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Affiliation(s)
- Dilip Sharma
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Ahmedabad, Gandhinagar 382355, Gujarat, India
| | - Pallab Bhattacharya
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Ahmedabad, Gandhinagar 382355, Gujarat, India
| | - Kiran Kalia
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Ahmedabad, Gandhinagar 382355, Gujarat, India.
| | - Vinod Tiwari
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Ahmedabad, Gandhinagar 382355, Gujarat, India.
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18
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Pradhan P, Upadhyay N, Tiwari A, Singh LP. Genetic and epigenetic modifications in the pathogenesis of diabetic retinopathy: a molecular link to regulate gene expression. ACTA ACUST UNITED AC 2016; 2:192-204. [PMID: 28691104 DOI: 10.15761/nfo.1000145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intensification in the frequency of diabetes and the associated vascular complications has been a root cause of blindness and visual impairment worldwide. One such vascular complication which has been the prominent cause of blindness; retinal vasculature, neuronal and glial abnormalities is diabetic retinopathy (DR), a chronic complicated outcome of Type 1 and Type 2 diabetes. It has also become clear that "genetic" variations in population alone can't explain the development and progression of diabetes and its complications including DR. DR experiences engagement of foremost mediators of diabetes such as hyperglycemia, oxidant stress, and inflammatory factors that lead to the dysregulation of "epigenetic" mechanisms involving histone acetylation and histone and DNA methylation, chromatin remodeling and expression of a complex set of stress-regulated and disease-associated genes. In addition, both elevated glucose concentration and insulin resistance leave a robust effect on epigenetic reprogramming of the endothelial cells too, since endothelium associated with the eye aids in maintaining the vascular homeostasis. Furthermore, several studies conducted on the disease suggest that the modifications of the epigenome might be the fundamental mechanism(s) for the proposed metabolic memory' resulting into prolonged gene expression for inflammation and cellular dysfunction even after attaining the glycemic control in diabetics. Henceforth, the present review focuses on the aspects of genetic and epigenetic alterations in genes such as vascular endothelial growth factor and aldose reductase considered being associated with DR. In addition, we discuss briefly the role of the thioredoxin-interacting protein TXNIP, which is strongly induced by high glucose and diabetes, in cellular oxidative stress and mitochondrial dysfunction potentially leading to chromatin remodeling and ocular complications of diabetes. The identification of disease-associated genes and their epigenetic regulations will lead to potential new drugs and gene therapies as well as personalized medicine to prevent or slow down the progression of DR.
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Affiliation(s)
- Priya Pradhan
- School of Biotechnology, Rajiv Gandhi Technical University, Bhopal, Madhya Pradesh, India
| | - Nisha Upadhyay
- School of Biotechnology, Rajiv Gandhi Technical University, Bhopal, Madhya Pradesh, India
| | - Archana Tiwari
- School of Biotechnology, Rajiv Gandhi Technical University, Bhopal, Madhya Pradesh, India
| | - Lalit P Singh
- Departments of Anatomy/Cell Biology and Ophthalmology, School of Medicine, Wayne State University, Detroit, MI, USA
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19
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Ahmadzadeh-Amiri A, Ahmadzadeh-Amiri A. Epigenetic Diabetic Vascular Complications. JOURNAL OF PEDIATRICS REVIEW 2016. [DOI: 10.17795/jpr-3375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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20
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Seyhan AA. microRNAs with different functions and roles in disease development and as potential biomarkers of diabetes: progress and challenges. MOLECULAR BIOSYSTEMS 2016; 11:1217-34. [PMID: 25765998 DOI: 10.1039/c5mb00064e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Biomarkers provide information on early detection of diseases, in determining individuals at risk of developing complications or subtyping individuals for disease phenotypes. In addition, biomarkers may lead to better treatment strategies, personalized therapy, and improved outcome. A major gap in the field of biomarker development is that we have not identified appropriate (minimally invasive, life-style independent and informative) biomarkers for the underlying disease process(es) that can be measured in readily accessible samples (e.g. serum, plasma, blood, urine). miRNAs function as regulators in wide ranging cellular and physiological functions and also participate in many physiopathological processes and thus have been linked to many diseases including diabetes, metabolic and cardiovascular diseases, cancer, neurodegenerative diseases, and autoimmunity. Many miRNAs have been shown to have predictive value as potential biomarkers in a variety of diseases including diabetes, which are detectable in some instances many years before the manifestation of disease. Although some technical challenges still remain, due to their availability in the circulation, relative stability, and ease of detection; miRNAs have emerged as a promising new class of biomarkers to provide information on early detection of disease, monitoring disease progression, in determining individual's risk of developing complications or subtyping individuals for disease phenotypes, and to monitor response to therapeutic interventions. As a final note, most of the miRNAs reported in the literature have not yet been validated in sufficiently powered and longitudinal studies for specificity for that particular disease.
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Affiliation(s)
- Attila A Seyhan
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Sanford Burnham Institute, 301 E. Princeton Street, Orlando, FL 32804, USA.
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21
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Chen Z. Progress and prospects of long noncoding RNAs in lipid homeostasis. Mol Metab 2015; 5:164-170. [PMID: 26977388 PMCID: PMC4770261 DOI: 10.1016/j.molmet.2015.12.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 12/10/2015] [Accepted: 12/20/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are a novel group of universally present, non-coding RNAs (>200 nt) that are increasingly recognized as key regulators of many physiological and pathological processes. SCOPE OF REVIEW Recent publications have shown that lncRNAs influence lipid homeostasis by controlling lipid metabolism in the liver and by regulating adipogenesis. lncRNAs control lipid metabolism-related gene expression by either base-pairing with RNA and DNA or by binding to proteins. MAJOR CONCLUSIONS The recent advances and future prospects in understanding the roles of lncRNAs in lipid homeostasis are discussed.
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Affiliation(s)
- Zheng Chen
- School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China.
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22
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Ciccacci C, Rufini S, Politi C, Novelli G, Forte V, Borgiani P. Could MicroRNA polymorphisms influence warfarin dosing? A pharmacogenetics study on mir133 genes. Thromb Res 2015; 136:367-70. [PMID: 26113018 DOI: 10.1016/j.thromres.2015.06.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/11/2015] [Accepted: 06/17/2015] [Indexed: 01/08/2023]
Abstract
MicroRNAs are small single stranded molecules that play a crucial role in regulation of physiological and pathological processes. Recent studies showed that VKORC1 gene contains an highly evolutionary conserved binding site for mir-133. Moreover, in human hepatocytes mir-133 is constitutively co-expressed with VKORC1. Since VKORC1 protein is the target of warfarin treatment, the aim of this study was to verify if genetic variations in MIR133A1, MIR133A2 and MIR133B could contribute to warfarin dose variability. By direct sequencing, we identified 4 SNPs in MIR133A2 gene and 1 SNP in MIR133B gene. Three SNPs in MIR133A2 were in complete linkage disequilibrium and correlated with warfarin dose: indeed, for each SNP, patients carrying the GA or AA genotype required a MWWD significantly higher than the wildtype genotype (P=0.019). We also inferred the haplotypes in MIR133A2 gene. The GC haplotype required a MWWD significantly lower than AT haplotype (P=0.012). The multiple linear regression analysis confirmed that rs45547937 (as tag SNP) in MIR133A2 could be involved in warfarin dosing variability, (P=0.016). These results seem to suggest that also polymorphisms in miRNA precursors may potentially affects drug response variability.
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Affiliation(s)
- Cinzia Ciccacci
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Italy.
| | - Sara Rufini
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Italy
| | - Cristina Politi
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Italy
| | - Vittorio Forte
- Center of Haemostasis and Thrombosis, Policlinico Tor Vergata, Rome, Italy
| | - Paola Borgiani
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Italy
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23
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Rönn T, Ling C. DNA methylation as a diagnostic and therapeutic target in the battle against Type 2 diabetes. Epigenomics 2015; 7:451-60. [DOI: 10.2217/epi.15.7] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Type 2 diabetes (T2D) develops due to insulin resistance and impaired insulin secretion, predominantly in genetically predisposed subjects exposed to nongenetic risk factors like obesity, physical inactivity and ageing. Emerging data suggest that epigenetics also play a key role in the pathogenesis of T2D. Genome-wide studies have identified altered DNA methylation patterns in pancreatic islets, skeletal muscle and adipose tissue from subjects with T2D compared with nondiabetic controls. Environmental factors known to affect T2D, including obesity, exercise and diet, have also been found to alter the human epigenome. Additionally, ageing and the intrauterine environment are associated with differential DNA methylation. Together, these data highlight a key role for epigenetics and particularly DNA methylation in the growing incidence of T2D.
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Affiliation(s)
- Tina Rönn
- Epigenetics & Diabetes, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, CRC, Jan Waldenströms gata 35, 205 02 Malmö, Sweden
| | - Charlotte Ling
- Epigenetics & Diabetes, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, CRC, Jan Waldenströms gata 35, 205 02 Malmö, Sweden
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24
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Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that have been found highly conserved among species. MiRNAs are able to negatively regulate gene expression through base pairing of 3' UTRs of their target genes. Therefore, miRNAs have been shown to play an important role in regulating various cellular activities. Over the past decade, substantial evidences have been obtained to show that miRNAs are aberrantly expressed in human malignancies and could act as "OncomiRs" or "Tumor suppressor miRs". In recent years, increasing number of studies have demonstrated the involvement of miRNAs in cancer metastasis. Many studies have shown that microRNAs could directly target genes playing a central role in epithelia-mesenchymal-transition (EMT), a cellular transformation process that allows cancer cells to acquire motility and invasiveness. EMT is considered an essential step driving the early phase of cancer metastasis. This review will summarize the recent findings and characterization of miRNAs that are involved in the regulation of EMT, migration, invasion and metastasis of cancer cells. Lastly, we will discuss potential use of miRNAs as diagnostic and prognostic biomarkers as well as therapeutic targets for cancer.
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Affiliation(s)
- Shih-Hsuan Chan
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County, 35053, Taiwan.
| | - Lu-Hai Wang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County, 35053, Taiwan.
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25
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Abstract
Diabetic vascular complications (DVCs) affecting several important organ systems of human body such as cardiovascular system contribute a major public health problem. Genetic factors contribute to the risk of diabetic nephropathy (DN). Genetics variants, structural variants (copy number variation) and epigenetic changes play important roles in the development of DN. Apart from nucleus genome, mitochondrial DNA (mtDNA) plays critical roles in regulation of development of DN. Epigenetic studies have indicated epigenetic changes in chromatin affecting gene transcription in response to environmental stimuli, which provided a large body of evidence of regulating development of diabetes mellitus. This review focused on the current knowledge of the genetic and epigenetic basis of DN. Ultimately, identification of genes or genetic loci, structural variants and epigenetic changes contributed to risk or protection of DN will benefit uncovering the complex mechanism underlying DN, with crucial implications for the development of personalized medicine to diabetes mellitus and its complications.
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Affiliation(s)
- Zi-Hui Tang
- Department of Endocrinology and Metabolism, Shanghai Tongji Hospital, Tongji University School of Medicine , Shanghai , China
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26
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Raciti GA, Nigro C, Longo M, Parrillo L, Miele C, Formisano P, Béguinot F. Personalized medicine and type 2 diabetes: lesson from epigenetics. Epigenomics 2015; 6:229-38. [PMID: 24811791 DOI: 10.2217/epi.14.10] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Similarly to genetic polymorphisms, epigenetic modifications may alter transcriptional activity and contribute to different traits of the Type 2 diabetes phenotype. The establishment of these epigenetic marks may precede diabetes onset and predict the disease. Current evidence now indicates that epigenetic differences represent markers of diabetes risk. Studies on epigenome plasticity revealed that cytokines and other metabolites, by affecting DNA methylation, may acutely reprogram gene expression and contribute to the Type 2 diabetes phenotype even in the adult life. The available evidence further indicates that epigenetic marks across the genome are subject to dynamic variations in response to environmental cues. Finally, different genes responsible for the interindividual variability in antidiabetic drug response are subjected to epigenetic regulation. Determining how specific epigenetic profiles determine diabetes is a challenging task. In the near future, the identification of epigenetic marks predictive of diabetes risk or response to treatment may offer unanticipated opportunities to personalize Type 2 diabetes management.
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Affiliation(s)
- Gregory Alexander Raciti
- Dipartimento di Scienze Mediche Traslazionali, 'Federico II' University of Naples Medical School & Istituto per l' Endocrinologia e l' Oncologia Sperimentale del CNR, Via Sergio Pansini, 5 - Naples, 80131, Italy
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27
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Li Y, Zhang Y, Li X, Shi L, Tao W, Shi L, Yang M, Wang X, Yang Y, Yao Y. Association study of polymorphisms in miRNAs with T2DM in Chinese population. Int J Med Sci 2015; 12:875-80. [PMID: 26640407 PMCID: PMC4643078 DOI: 10.7150/ijms.12954] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/20/2015] [Indexed: 12/19/2022] Open
Abstract
Accumulated evidence indicates that microRNA (miRNA or miR) is involved in the development of type 2 diabetes (T2DM). Several studies have shown that single nucleotide polymorphisms (SNPs) located in miRNAs are associated with T2DM in Caucasian populations. The association studies of miRNA's SNPs with T2DM in Asian are rarely reported, and there are distinct genetic differences between Caucasian and Asian populations. The focus of this study, therefore, is the association of T2DM with five SNPs (rs895819 in miR-27a, rs531564 in miR-124a, rs11888095 in miR-128a, rs3820455 in miR-194a and rs2910164 in miR-146a) located in five miRNAs in a Han Chinese population. A total of 738 subjects with T2DM and 610 non-diabetic subjects were genotyped using the TaqMan method. Next, the associations between the five SNPs with T2DM and individual metabolic traits were evaluated. Our data showed that the C allele of rs531564 in miR-124a may protect against T2DM (P=0.009, OR=0.758; 95%CI: 0.616-0.933). Conversely, the C allele of rs2910164 in miR-146a may increase the risk of developing T2DM (P<0.001, OR=1.459; 95%CI: 1.244-1.712). However, these five SNPs did not exhibit significant associations with individual metabolic traits in either the T2DM or non-diabetic groups. Our results revealed that genetic variations in miRNAs were associated with T2DM susceptibility in a Han Chinese population, and these results highlight the need to study the functional effects of these variants in miRNAs on the risk of developing T2DM.
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Affiliation(s)
- Yiping Li
- 1. Department of Endocrinology and Metabolism, The Second People's Hospital of Yunnan Province & The Fourth Affiliated Hospital of Kunming Medical University, Kunming 650021, Yunnan, China ; 2. Key Laboratory of Fertility Regulation and Eugenics of Minority Research of Yunnan Province, Kunming 650091, Yunnan, China
| | - Yu Zhang
- 3. Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Xianli Li
- 1. Department of Endocrinology and Metabolism, The Second People's Hospital of Yunnan Province & The Fourth Affiliated Hospital of Kunming Medical University, Kunming 650021, Yunnan, China
| | - Li Shi
- 3. Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Wenyu Tao
- 1. Department of Endocrinology and Metabolism, The Second People's Hospital of Yunnan Province & The Fourth Affiliated Hospital of Kunming Medical University, Kunming 650021, Yunnan, China
| | - Lei Shi
- 3. Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Man Yang
- 1. Department of Endocrinology and Metabolism, The Second People's Hospital of Yunnan Province & The Fourth Affiliated Hospital of Kunming Medical University, Kunming 650021, Yunnan, China
| | - Xiaoling Wang
- 1. Department of Endocrinology and Metabolism, The Second People's Hospital of Yunnan Province & The Fourth Affiliated Hospital of Kunming Medical University, Kunming 650021, Yunnan, China
| | - Ying Yang
- 1. Department of Endocrinology and Metabolism, The Second People's Hospital of Yunnan Province & The Fourth Affiliated Hospital of Kunming Medical University, Kunming 650021, Yunnan, China
| | - Yufeng Yao
- 3. Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
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Tang ZH, Wang L, Zeng F, Zhang K. Human genetics of diabetic retinopathy. J Endocrinol Invest 2014; 37:1165-74. [PMID: 25201002 DOI: 10.1007/s40618-014-0172-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 08/25/2014] [Indexed: 01/03/2023]
Abstract
There is evidence demonstrating that genetic factors contribute to the risk of diabetic retinopathy (DR). Genetics variants, structural variants (copy number variation, CNV) and epigenetic changes play important roles in the development of DR. Genetic linkage and association studies have uncovered a number of genetic loci and common genetic variants susceptibility to DR. CNV and interactions of gene by environment have also been detected by association analysis. Apart from nucleus genome, mitochondrial DNA plays critical roles in regulation of development of DR. Epigenetic studies have indicated epigenetic changes in chromatin affecting gene transcription in response to environmental stimuli, which provided a large body of evidence of regulating development of diabetes mellitus. Identification of genetic variants and epigenetic changes contributed to risk or protection of DR will benefit uncovering the complex mechanism underlying DR. This review focused on the current knowledge of the genetic and epigenetic basis of DR.
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Affiliation(s)
- Z-H Tang
- Department of Endocrinology and Metabolism, Shanghai Tongji Hospital, Tongji University School of Medicine, Room 517 Building 2nd, NO. 389 Xincun Road, Shanghai, 200063, China,
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Zhang Y, Zhou D, He J. MicroRNA Sensor Based on Magnetic Beads and Enzymatic Probes. INTERNATIONAL JOURNAL OF NANOSCIENCE 2014. [DOI: 10.1142/s0219581x1460014x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
MicroRNAs are associated with multiple cellular processes and diseases. Here, we designed a highly sensitive, magnetically retrievable biosensor using magnetic beads (MBs) as a model RNA sensor. The assay utilized two biotinylated probes, which were hybridized to the complementary target miRNA in a sandwich assay format. One of the biotinylated ends of the hybridization complex was immobilized onto the surface of a NeutrAvidin (NAV) coated MB and the other biotinylated end was conjugated to HRP via NAV-biotin interaction. The results were presented by colorimetric absorbance of the resorufin product from amplex red oxidation. We show that by combining the use of MBs as well as bio-specific immobilization, the sensitivity of miRNA detection is down to 100 pM. This model HRP-MBs system can be used for simple, rapid colorimetric quantification of low level DNA/RNA or other small molecules.
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Affiliation(s)
- Yue Zhang
- Functional Nanomaterials Laboratory, Center for Micro/Nanomaterials and Technology, Technical Institute of Physics and Chemistry (TIPC), CAS, Zhongguancundonglu 29, Haidianqu, Beijing 100190, P. R. China
| | - Dejian Zhou
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Junhui He
- Functional Nanomaterials Laboratory, Center for Micro/Nanomaterials and Technology, Technical Institute of Physics and Chemistry (TIPC), CAS, Zhongguancundonglu 29, Haidianqu, Beijing 100190, P. R. China
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Zeng J, Chen B. Epigenetic mechanisms in the pathogenesis of diabetic retinopathy. Ophthalmologica 2014; 232:1-9. [PMID: 24714375 DOI: 10.1159/000357824] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 12/08/2013] [Indexed: 11/19/2022]
Abstract
Diabetic retinopathy (DR), which arises as a result of an increasing incidence of diabetes mellitus, has gradually become a common disease. Due to its complex pathogenesis, the treatment means of DR are very limited. The findings of several studies have shown that instituting tight glycemic control in diabetic patients does not immediately benefit the progression of retinopathy, and the benefits of good control persist beyond the period of good glycemic control. This has led to the concept of persistent epigenetic changes. Epigenetics has now become an increasingly important area of biomedical research. Recently, important roles of various epigenetic mechanisms have been identified in the pathogenesis of diabetes and its complications. The aim of this review is to provide an overview of the epigenetics and epigenetic mechanisms in diabetes and diabetes complications, and the focus is on the emerging evidence for aberrant epigenetic mechanisms in DR.
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Affiliation(s)
- Jun Zeng
- Department of Ophthalmology, Second Xiangya Hospital, Central South University, Changsha City, PR China
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Ciccacci C, Di Fusco D, Cacciotti L, Morganti R, D'Amato C, Greco C, Rufini S, Novelli G, Sangiuolo F, Spallone V, Borgiani P. MicroRNA genetic variations: association with type 2 diabetes. Acta Diabetol 2013; 50:867-72. [PMID: 23532299 DOI: 10.1007/s00592-013-0469-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/06/2013] [Indexed: 12/13/2022]
Abstract
MicroRNAs are small single-stranded molecules that have emerged as important genomic regulators in different pathways. Different studies have shown that they are implicated in the metabolism and glucose homeostasis, and therefore, they could also be involved in the pathogenesis of metabolic disorders such as type 2 diabetes (T2DM). The aim of this study was to verify whether genetic variations in candidate microRNA (miRNA or miR) genes could contribute to T2DM susceptibility. We have selected 13 miRNAs as candidate loci according to literature data and to a computational analysis. MicroRNA genes were analyzed by direct sequencing in a cohort of 163 Italian T2DM patients and 185 healthy controls. We identified 6 novel variants never described before and 9 SNPs already described in databases. Five newly identified variants were found only in the cases group. We performed a case/control association study to test the associations of particular alleles/genotypes of identified SNPs with the disease. Two polymorphisms were associated with T2DM susceptibility: in particular, the G allele of rs895819 in hsa-mir-27a has shown a significantly protective effect (OR = 0.58 and P = 0.008), while the G allele of rs531564 in hsa-mir-124a appears to be a risk allele (OR = 2.15, P = 0.008). This is the first report indicating that genetic polymorphisms in miRNA regions could contribute to T2DM susceptibility.
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Affiliation(s)
- Cinzia Ciccacci
- Department of Biomedicine and Prevention, Genetics Section, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
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Kumar M, Nath S, Prasad HK, Sharma GD, Li Y. MicroRNAs: a new ray of hope for diabetes mellitus. Protein Cell 2012; 3:726-38. [PMID: 23055040 DOI: 10.1007/s13238-012-2055-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 07/01/2012] [Indexed: 12/28/2022] Open
Abstract
Diabetes mellitus has become one of the most common chronic diseases, thereby posing a major challenge to global health. Characterized by high levels of blood glucose (hyperglycemia), diabetes usually results from a loss of insulin-producing β-cells in the pancreas, leading to a deficiency of insulin (type 1 diabetes), or loss of insulin sensitivity (type 2 diabetes). Both types of diabetes have serious secondary complications, such as microvascular abnormalities, cardiovascular dysfunction, and kidney failure. Various complex factors, such as genetic and environmental factors, are associated with the pathophysiology of diabetes. Over the past two decades, the role of small, single-stranded noncoding microRNAs in various metabolic disorders, especially diabetes mellitus and its complications, has gained widespread attention in the scientific community. Discovered first as an endogenous regulator of development in the nematode Caenorhabditis elegans, these small RNAs post-transcriptionally suppress mRNA target expression. In this review, we discuss the potential roles of different microRNAs in diabetes and diabetes-related complications.
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Affiliation(s)
- Munish Kumar
- Department of Biotechnology, Assam University, Silchar, India.
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Park SG, Kwon KH, Choi SS. Analysis of putative miRNA function using a novel approach, GAPPS-miRTarGE. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0233-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Sadi G, Eryilmaz N, Tütüncüoğlu E, Cingir Ş, Güray T. Changes in expression profiles of antioxidant enzymes in diabetic rat kidneys. Diabetes Metab Res Rev 2012; 28:228-35. [PMID: 22057777 DOI: 10.1002/dmrr.1302] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND In diabetes mellitus, increased formation of reactive oxygen species due to high level of glucose in both blood plasma and tissues creates oxidative stress and damages the tissues. Antioxidants together with the antioxidant enzymes are very important in order to protect the cells against oxidative damage. METHODS Differential expressions of both mRNA and proteins of major antioxidant enzymes in streptozotocin-induced diabetic rat kidneys were measured with the help of real-time polymerase chain reaction and western blot analysis, respectively. Furthermore, effects of two strong antioxidants α-lipoic acid, vitamin C and their combination on the regulation of both expressions and the activities of antioxidant enzymes were also studied. RESULTS In diabetic rat kidney tissue, both catalase and glutathione peroxidase activities were reduced (although mRNA expression for both was greatly increased) when compared with controls. No significant change was observed in superoxide dismutase (SOD) activity. Alpha-lipoic acid increased catalase activity towards the control values. Combined administration of alpha-lipoic acid and vitamin C increased the activities of both catalase and SOD, demonstrating a posttranslational effect. Glutathione concentrations were decreased in diabetic kidney; alpha-lipoic acid treatment partially restored the glutathione levels. CONCLUSIONS All data showed the importance of post-transcriptional and translational regulation of the antioxidant enzyme activities against oxidative stress that is associated with diabetes.
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Affiliation(s)
- Gökhan Sadi
- Department of Biology, Karamanoğlu Mehmetbey University, Karaman, Turkey.
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Wang X, Prins BP, Sõber S, Laan M, Snieder H. Beyond genome-wide association studies: new strategies for identifying genetic determinants of hypertension. Curr Hypertens Rep 2011; 13:442-51. [PMID: 21953487 PMCID: PMC3212682 DOI: 10.1007/s11906-011-0230-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Genetic linkage and association methods have long been the most important tools for gene identification in humans. These approaches can either be hypothesis-based (i.e., candidate-gene studies) or hypothesis-free (i.e., genome-wide studies). The first part of this review offers an overview of the latest successes in gene finding for blood pressure (BP) and essential hypertension using these DNA sequence-based discovery techniques. We further emphasize the importance of post-genome-wide association study (post-GWAS) analysis, which aims to prioritize genetic variants for functional follow-up. Whole-genome next-generation sequencing will eventually be necessary to provide a more comprehensive picture of all DNA variants affecting BP and hypertension. The second part of this review discusses promising novel approaches that move beyond the DNA sequence and aim to discover BP genes that are differentially regulated by epigenetic mechanisms, including microRNAs, histone modification, and methylation.
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Affiliation(s)
- Xiaoling Wang
- Georgia Prevention Institute, Department of Pediatrics, Medical College of Georgia, Augusta, GA USA
| | - Bram P. Prins
- Unit of Genetic Epidemiology & Bioinformatics, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Siim Sõber
- Human Molecular Genetics group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maris Laan
- Human Molecular Genetics group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Harold Snieder
- Unit of Genetic Epidemiology & Bioinformatics, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30.001, 9700 RB Groningen, The Netherlands
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Rantalainen M, Herrera BM, Nicholson G, Bowden R, Wills QF, Min JL, Neville MJ, Barrett A, Allen M, Rayner NW, Fleckner J, McCarthy MI, Zondervan KT, Karpe F, Holmes CC, Lindgren CM. MicroRNA expression in abdominal and gluteal adipose tissue is associated with mRNA expression levels and partly genetically driven. PLoS One 2011; 6:e27338. [PMID: 22102887 PMCID: PMC3216936 DOI: 10.1371/journal.pone.0027338] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 10/14/2011] [Indexed: 12/24/2022] Open
Abstract
To understand how miRNAs contribute to the molecular phenotype of adipose tissues and related traits, we performed global miRNA expression profiling in subcutaneous abdominal and gluteal adipose tissue of 70 human subjects and characterised which miRNAs were differentially expressed between these tissues. We found that 12% of the miRNAs were significantly differentially expressed between abdominal and gluteal adipose tissue (FDR adjusted p<0.05) in the primary study, of which 59 replicated in a follow-up study of 40 additional subjects. Further, 14 miRNAs were found to be associated with metabolic syndrome case-control status in abdominal tissue and three of these replicated (primary study: FDR adjusted p<0.05, replication: p<0.05 and directionally consistent effect). Genome-wide genotyping was performed in the 70 subjects to enable miRNA expression quantitative trait loci (eQTL) analysis. Candidate miRNA eQTLs were followed-up in the additional 40 subjects and six significant, independent cis-located miRNA eQTLs (primary study: p<0.001; replication: p<0.05 and directionally consistent effect) were identified. Finally, global mRNA expression profiling was performed in both tissues to enable association analysis between miRNA and target mRNA expression levels. We find 22% miRNAs in abdominal and 9% miRNAs in gluteal adipose tissue with expression levels significantly associated with the expression of corresponding target mRNAs (FDR adjusted p<0.05). Taken together, our results indicate a clear difference in the miRNA molecular phenotypic profile of abdominal and gluteal adipose tissue, that the expressions of some miRNAs are influenced by cis-located genetic variants and that miRNAs are associated with expression levels of their predicted mRNA targets.
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Affiliation(s)
- Mattias Rantalainen
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Blanca M. Herrera
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - George Nicholson
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Rory Bowden
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Quin F. Wills
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Josine L. Min
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matt J. Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Headington, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, ORH Trust, Churchill Hospital, Oxford, United Kingdom
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Headington, Oxford, United Kingdom
| | - Maxine Allen
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Headington, Oxford, United Kingdom
| | - Nigel W. Rayner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Headington, Oxford, United Kingdom
| | | | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Headington, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, ORH Trust, Churchill Hospital, Oxford, United Kingdom
| | - Krina T. Zondervan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Headington, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, ORH Trust, Churchill Hospital, Oxford, United Kingdom
| | - Chris C. Holmes
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- MRC Mammalian Genetics Unit, MRC Harwell, Harwell, Oxford, United Kingdom
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Manolopoulos VG, Ragia G, Tavridou A. Pharmacogenomics of oral antidiabetic medications: current data and pharmacoepigenomic perspective. Pharmacogenomics 2011; 12:1161-91. [PMID: 21843065 DOI: 10.2217/pgs.11.65] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is an increasingly prevalent disease. Several classes of drugs are currently available to treat T2DM patients; however, clinical response to these drugs often exhibits significant variation among individuals. For the oral antidiabetic drug classes of sulfonylureas, nonsulfonylurea insulin secretagogs, biguanides and thiazolidinediones, pharmacogenomic evidence has accumulated demonstrating an association between specific gene polymorphisms and interindividual variability in their therapeutic and adverse reaction effects. These polymorphisms are in genes of molecules involved in metabolism, transport and therapeutic mechanisms of the aforementioned drugs. Overall, it appears that pharmacogenomics has the potential to improve the management of T2DM and help clinicians in the effective prescribing of oral antidiabetic medications. Although pharmacogenomics can explain some of the heterogeneity in dose requirements, response and incidence of adverse effects of drugs between individuals, it is now clearly understood that much of the diversity in drug effects cannot be solely explained by studying the genomic diversity. Epigenomics, the field that focuses on nongenomic modifications that influence gene expression, may expand the scope of pharmacogenomics towards optimization of drug therapy. Therefore, pharmacoepigenomics, the combined analysis of genetic variations and epigenetic modifications, holds promise for the realization of personalized medicine. Although pharmacoepigenomics has so far been evaluated mainly in cancer pharmacotherapy, studies on epigenomic modifications during T2DM development provide useful data on the potential of pharmacoepigenomics to elucidate the mechanisms underlying interindividual response to oral antidiabetic treatment. In summary, the present article focuses on available data from pharmacogenomic studies of oral antidiabetic drugs and also provides an overview of T2DM epigenomic research, which has the potential to boost the development of pharmacoepigenomics in antidiabetic treatment.
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Affiliation(s)
- Vangelis G Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Dragana Campus, 68100 Alexandroupolis, Greece.
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Rácz Z, Kaucsár T, Hamar P. The huge world of small RNAs: regulating networks of microRNAs (review). ACTA ACUST UNITED AC 2011; 98:243-51. [PMID: 21893463 DOI: 10.1556/aphysiol.98.2011.3.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
MicroRNAs (miRNAs) are a recently discovered class of small, non-coding RNAs which do not code proteins. MiRNAs regulate gene expression by inhibiting protein translation from the messenger RNA. MiRNAs may function in networks, forming a complex relationship with diseases. Furthermore, specific miRNAs have significant correlation with diseases of divergent origin. After identification of disease-associated miRNAs, their tissue expression could be altered in a beneficial way by inhibiting or mimicking their effects. Thus, modifying the expression of miRNAs is a potential future gene-therapeutic tool to influence post-transcriptional regulation of multiple genes in a single therapy. In this review we introduce the biogenesis, mechanism of action and future aspects of miRNAs. Research on the post-transcriptional regulation of gene expression by miRNA may reshape our understanding of diseases and consequently may bring new diagnostic markers and therapeutic agents. Therapeutic use of miRNAs is already under clinical investigation in RNA interference trials.
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Affiliation(s)
- Zs Rácz
- Semmelweis University Institute of Pathophysiology, Faculty of Medicine, Budapest, Hungary
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Abstract
There has been a rapid increase in the incidence of diabetes as well the associated vascular complications. Both genetic and environmental factors have been implicated in these pathologies. Increasing evidence suggests that epigenetic factors play a key role in the complex interplay between genes and the environment. Actions of major pathological mediators of diabetes and its complications such as hyperglycaemia, oxidant stress, and inflammatory factors can lead to dysregulated epigenetic mechanisms that affect chromatin structure and gene expression. Furthermore, persistence of this altered state of the epigenome may be the underlying mechanism contributing to a 'metabolic memory' that results in chronic inflammation and vascular dysfunction in diabetes even after achieving glycaemic control. Further examination of epigenetic mechanisms by also taking advantage of recently developed next-generation sequencing technologies can provide novel insights into the pathology of diabetes and its complications and lead to the discovery of much needed new drug targets for these diseases. In this review, we highlight the role of epigenetics in diabetes and its vascular complications, and recent technological advances that have significantly accelerated the field.
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Affiliation(s)
- Marpadga A Reddy
- Department of Diabetes, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
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42
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Huang D, Zhou X, Lyon CJ, Hsueh WA, Wong STC. MicroRNA-integrated and network-embedded gene selection with diffusion distance. PLoS One 2010; 5:e13748. [PMID: 21060785 PMCID: PMC2966417 DOI: 10.1371/journal.pone.0013748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Accepted: 05/17/2010] [Indexed: 11/19/2022] Open
Abstract
Gene network information has been used to improve gene selection in microarray-based studies by selecting marker genes based both on their expression and the coordinate expression of genes within their gene network under a given condition. Here we propose a new network-embedded gene selection model. In this model, we first address the limitations of microarray data. Microarray data, although widely used for gene selection, measures only mRNA abundance, which does not always reflect the ultimate gene phenotype, since it does not account for post-transcriptional effects. To overcome this important (critical in certain cases) but ignored-in-almost-all-existing-studies limitation, we design a new strategy to integrate together microarray data with the information of microRNA, the major post-transcriptional regulatory factor. We also handle the challenges led by gene collaboration mechanism. To incorporate the biological facts that genes without direct interactions may work closely due to signal transduction and that two genes may be functionally connected through multi paths, we adopt the concept of diffusion distance. This concept permits us to simulate biological signal propagation and therefore to estimate the collaboration probability for all gene pairs, directly or indirectly-connected, according to multi paths connecting them. We demonstrate, using type 2 diabetes (DM2) as an example, that the proposed strategies can enhance the identification of functional gene partners, which is the key issue in a network-embedded gene selection model. More importantly, we show that our gene selection model outperforms related ones. Genes selected by our model 1) have improved classification capability; 2) agree with biological evidence of DM2-association; and 3) are involved in many well-known DM2-associated pathways.
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Affiliation(s)
- Di Huang
- Bioinformatics Core, The Methodist Hospital Research Institute, Weill Medical College, Cornell University, Houston, Texas, United States of America
| | - Xiaobo Zhou
- Bioinformatics Core, The Methodist Hospital Research Institute, Weill Medical College, Cornell University, Houston, Texas, United States of America
| | - Christopher J. Lyon
- Diabetes Research Center, The Methodist Hospital Research Institute, Weill Medical College, Cornell University, Houston, Texas, United States of America
| | - Willa A. Hsueh
- Diabetes Research Center, The Methodist Hospital Research Institute, Weill Medical College, Cornell University, Houston, Texas, United States of America
| | - Stephen T. C. Wong
- Bioinformatics Core, The Methodist Hospital Research Institute, Weill Medical College, Cornell University, Houston, Texas, United States of America
- * E-mail:
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Ortiz A, Ucero AC, Egido J. Unravelling fibrosis: two newcomers and an old foe. Nephrol Dial Transplant 2010; 25:3492-5. [PMID: 20833689 DOI: 10.1093/ndt/gfq518] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Alberto Ortiz
- Dpto de Nefrología Experimental y Patología Vascular, IIS-Fundación Jiménez Díaz, Av/ Reyes Católicos, Madrid, Spain
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Qavi AJ, Bailey RC. Multiplexed detection and label-free quantitation of microRNAs using arrays of silicon photonic microring resonators. Angew Chem Int Ed Engl 2010; 49:4608-11. [PMID: 20491114 PMCID: PMC2994205 DOI: 10.1002/anie.201001712] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Abraham J. Qavi
- Department of Chemistry, Institute for Genomic Biology, and Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Illinois, 61801 (United States), Fax: (217) 265-6290
| | - Ryan C. Bailey
- Department of Chemistry, Institute for Genomic Biology, and Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Illinois, 61801 (United States), Fax: (217) 265-6290
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Qavi A, Bailey R. Multiplexed Detection and Label-Free Quantitation of MicroRNAs Using Arrays of Silicon Photonic Microring Resonators. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001712] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Villeneuve LM, Natarajan R. The role of epigenetics in the pathology of diabetic complications. Am J Physiol Renal Physiol 2010; 299:F14-25. [PMID: 20462972 DOI: 10.1152/ajprenal.00200.2010] [Citation(s) in RCA: 227] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Diabetes is associated with significantly accelerated rates of several debilitating microvascular complications such as nephropathy, retinopathy, and neuropathy, and macrovascular complications such as atherosclerosis and stroke. While several studies have been devoted to the evaluation of genetic factors related to type 1 and type 2 diabetes and associated complications, much less is known about epigenetic changes that occur without alterations in the DNA sequence. Environmental factors and nutrition have been implicated in diabetes and can also affect epigenetic states. Exciting research has shown that epigenetic changes in chromatin can affect gene transcription in response to environmental stimuli, and changes in key chromatin histone methylation patterns have been noted under diabetic conditions. Reports also suggest that epigenetics may be involved in the phenomenon of metabolic memory observed in clinic trials and animal studies. Further exploration into epigenetic mechanisms can yield new insights into the pathogenesis of diabetes and its complications and uncover potential therapeutic targets and treatment options to prevent the continued development of diabetic complications even after glucose control has been achieved.
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Affiliation(s)
- Louisa M Villeneuve
- Department of Diabetes, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
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Torres A, Torres K, Maciejewski R, Harvey WH. MicroRNAs and their role in gynecological tumors. Med Res Rev 2010; 31:895-923. [PMID: 20358579 DOI: 10.1002/med.20205] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There have been only few events in the history of molecular biology that could be compared to the discovery of microRNAs and their role in cell physiology and pathology. MicroRNAs are small, single-stranded, noncoding RNAs composed of 19-25 nucleotides (∼22 nt), which have been proven to regulate gene expression at the posttranscriptional level. The regulatory function of microRNAs was demonstrated in normal and diseased conditions. In particular, it has been linked to cell cycle regulation, cell proliferation and differentiation, inflammatory response, and apoptosis. Altered expression profiles of microRNA have been observed in many pathologies, including diabetes, rheumatoid arthritis, and several cancers. To date, more than 700 human microRNAs have been identified and in silico-based analyses estimate at least 500 more to be identified. The purpose of this review is to present the current perspective on microRNAs structure and biogenesis as well as their contribution to the etiopathogenesis of gynecological tumors. We discuss results of the recent publications that indicate possibilities of microRNAs use as novel markers for tumors screening, early diagnosis, and treatment monitoring. The possible utilization of microRNAs as prognostic factors and specific therapy targets is also reviewed.
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Affiliation(s)
- Anna Torres
- Laboratory of Biostructure, Human Anatomy Department, Medical University of Lublin, Lublin, Poland.
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Ryan FP. An alternative approach to medical genetics based on modern evolutionary biology. Part 5: epigenetics and genomics. J R Soc Med 2009; 102:531-7. [PMID: 19966129 DOI: 10.1258/jrsm.2009.090365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Frank P Ryan
- Sheffield Primary Care Trust and Department of Animal and Plant Sciences, Sheffield University.
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